LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide

units		real
atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	data.peptide
Reading data file ...
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     7 = max # of 1-3 neighbors
    14 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.011 seconds

neighbor	2.0 bin
neigh_modify	delay 5

timestep	2.0

group		peptide type <= 12
84 atoms in group peptide
group		one id 2 4 5 6
4 atoms in group one
group		two id 80 82 83 84
4 atoms in group two
group		ref id 37
1 atoms in group ref
group		colvar union one two ref
9 atoms in group colvar

fix		1 all nvt temp  275.0 275.0 100.0 tchain 1

shell "rm -f out*.colvars.*"
fix		2 all colvars peptide.colvars
----------------------------------------------------------------------
Initializing the collective variables module, version 2025-04-30.
Please cite Fiorin et al, Mol Phys 2013:
  https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Summary of compile-time features available in this build:
  - C++ language version: 201703
  - Multiple replicas: not available
  - Lepton custom functions: available
  - Tcl interpreter: not available
Using LAMMPS interface, version "2025-03-31".
fix		2a ref setforce 0.0 0.0 0.0

fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
      19 = # of size 2 clusters
       6 = # of size 3 clusters
       3 = # of size 4 clusters
     640 = # of frozen angles
  find clusters CPU = 0.000 seconds

#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id

thermo_style	custom step temp etotal pe ke epair ebond f_2
thermo		10


run		100
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars":
# units = "" [default]
# smp = "cvcs" [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
  Initializing a new collective variable.
  # name = "one"
    Initializing a new "distance" component.
    # name = "" [default]
    # componentCoeff = 1 [default]
    # componentExp = 1 [default]
    # period = 0 [default]
    # wrapAround = 0 [default]
    # forceNoPBC = off [default]
    # scalable = on [default]
      Initializing atom group "group1".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group1" defined with 4 atoms requested.
      Initializing atom group "group2".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group2" defined with 1 atoms requested.
    # oneSiteSystemForce = off [default]
    # oneSiteTotalForce = off [default]
  All components initialized.
  # timeStepFactor = 1 [default]
  # width = 1 [default]
  # lowerBoundary = 0 [default]
  # upperBoundary = 1 [default]
  # hardLowerBoundary = on [default]
  # hardUpperBoundary = off [default]
  # expandBoundaries = off [default]
  # extendedLagrangian = off [default]
  # outputValue = on [default]
  # outputVelocity = off [default]
  # outputTotalForce = off [default]
  # outputAppliedForce = off [default]
  # subtractAppliedForce = off [default]
  # runAve = off [default]
  # corrFunc = off [default]
----------------------------------------------------------------------
  Initializing a new collective variable.
  # name = "two"
    Initializing a new "distance" component.
    # name = "" [default]
    # componentCoeff = 1 [default]
    # componentExp = 1 [default]
    # period = 0 [default]
    # wrapAround = 0 [default]
    # forceNoPBC = off [default]
    # scalable = on [default]
      Initializing atom group "group1".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group1" defined with 4 atoms requested.
      Initializing atom group "group2".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group2" defined with 1 atoms requested.
    # oneSiteSystemForce = off [default]
    # oneSiteTotalForce = off [default]
  All components initialized.
  # timeStepFactor = 1 [default]
  # width = 1 [default]
  # lowerBoundary = 0 [default]
  # upperBoundary = 1 [default]
  # hardLowerBoundary = on [default]
  # hardUpperBoundary = off [default]
  # expandBoundaries = off [default]
  # extendedLagrangian = off [default]
  # outputValue = on [default]
  # outputVelocity = off [default]
  # outputTotalForce = off [default]
  # outputAppliedForce = off [default]
  # subtractAppliedForce = off [default]
  # runAve = off [default]
  # corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 2 in total.
----------------------------------------------------------------------
  Initializing a new "harmonic" instance.
  # name = "h_pot"
  # colvars = { one, two }
  # stepZeroData = off [default]
  # outputEnergy = off [default]
  # outputFreq = 1000 [default]
  # timeStepFactor = 1 [default]
  # writeTISamples = off [default]
  # writeTIPMF = off [default]
  # centers = { 10, 10 }
  # targetCenters = { 10, 10 } [default]
  # outputCenters = off [default]
  # forceConstant = 100
  # decoupling = off [default]
  # targetForceConstant = -1 [default]
  The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
  The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 0, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
The final output state file will be "out.colvars.state".
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
SHAKE stats (type/ave/delta/count) on step 0
Bond:    4   1.111     1.44264e-05        9
Bond:    6   0.996998  7.26967e-06        6
Bond:    8   1.08      1.32536e-05        7
Bond:   10   1.111     1.22749e-05        8
Bond:   12   1.08      1.11767e-05        9
Bond:   14   0.96      0                  1
Bond:   18   0.957206  4.37979e-05     1280
Angle:  31   104.519   0.00396029       640
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
   Step          Temp          TotEng         PotEng         KinEng         E_pair         E_bond          f_2      
         0   282.10052     -5237.458      -6372.3765      1134.9186     -6442.7679      16.557152      292.14604    
        10   305.06149     -5058.8971     -6286.1899      1227.2929     -6413.1019      58.8499        103.38345    
        20   311.00516     -4999.0612     -6250.266       1251.2048     -6417.1021      47.695297      36.699695    
        30   314.22337     -4993.7011     -6257.8532      1264.152      -6421.9678      35.344144      10.563932    
        40   297.87492     -5020.8375     -6219.2181      1198.3806     -6389.8526      27.723134      3.8354514    
        50   304.0207      -5056.2575     -6279.3632      1223.1057     -6456.8213      55.459507      0.20678213   
        60   285.92576     -5104.046      -6254.354       1150.3079     -6435.5813      32.76723       0.69352954   
        70   277.83519     -5163.9756     -6281.7343      1117.7587     -6447.7031      39.627168      11.433604    
        80   267.51495     -5206.4046     -6282.644       1076.2394     -6456.6368      31.611883      6.355418     
        90   278.15579     -5245.3825     -6364.431       1119.0485     -6499.8063      28.849773      0.36941575   
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.11098   8.97155e-05        9
Bond:    6   0.996996  1.00568e-05        6
Bond:    8   1.08      6.02345e-06        7
Bond:   10   1.111     1.84253e-05        8
Bond:   12   1.08      7.2713e-06         9
Bond:   14   0.959996  0                  1
Bond:   18   0.957198  3.36079e-05     1280
Angle:  31   104.52    0.0030599        640
       100   260.10611     -5292.6885     -6339.1214      1046.4329     -6471.6733      25.362042      0.2198733    
Saving collective variables state to "out.colvars.state".
Loop time of 0.875226 on 1 procs for 100 steps with 2004 atoms

Performance: 19.743 ns/day, 1.216 hours/ns, 114.256 timesteps/s, 228.970 katom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.69729    | 0.69729    | 0.69729    |   0.0 | 79.67
Bond    | 0.001366   | 0.001366   | 0.001366   |   0.0 |  0.16
Kspace  | 0.041098   | 0.041098   | 0.041098   |   0.0 |  4.70
Neigh   | 0.12128    | 0.12128    | 0.12128    |   0.0 | 13.86
Comm    | 0.0033425  | 0.0033425  | 0.0033425  |   0.0 |  0.38
Output  | 0.00013746 | 0.00013746 | 0.00013746 |   0.0 |  0.02
Modify  | 0.010211   | 0.010211   | 0.010211   |   0.0 |  1.17
Other   |            | 0.0005003  |            |       |  0.06

Nlocal:           2004 ave        2004 max        2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          11124 ave       11124 max       11124 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         708237 ave      708237 max      708237 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708237
Ave neighs/atom = 353.41168
Ave special neighs/atom = 2.3403194
Neighbor list builds = 12
Dangerous builds = 2

run     100

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Colvars module (Fiorin2013, plus other works listed for specific features)


% Colvars module:
% Colvars-LAMMPS interface:
% Harmonic colvar bias implementation:
% Optimal rotation via flexible fitting:
% distance colvar component:

@article{Fiorin2013,
  author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
  title = {Using collective variables to drive molecular dynamics simulations},
  journal = {Mol. Phys.},
  year = {2013},
  volume = {111},
  number = {22-23},
  pages = {3345--3362},
  publisher = {Taylor & Francis},
  doi = {10.1080/00268976.2013.813594},
  url = {https://doi.org/10.1080/00268976.2013.813594}
}


% LAMMPS engine:

@article{Thompson2022,
  title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
  author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
  journal = {Comp. Phys. Comm.},
  volume = {271},
  pages = {108171},
  year = {2022},
  doi = {10.1016/j.cpc.2021.108171},
  url = {https://doi.org/10.1016/j.cpc.2021.108171}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Current simulation parameters: initial step = 100, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.11098   8.97155e-05        9
Bond:    6   0.996996  1.00568e-05        6
Bond:    8   1.08      6.02345e-06        7
Bond:   10   1.111     1.84253e-05        8
Bond:   12   1.08      7.2713e-06         9
Bond:   14   0.959996  0                  1
Bond:   18   0.957198  3.36079e-05     1280
Angle:  31   104.52    0.0030599        640
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
   Step          Temp          TotEng         PotEng         KinEng         E_pair         E_bond          f_2      
       100   260.10611     -5292.6885     -6339.1214      1046.4329     -6471.6733      25.362042      0.2198733    
       110   266.2644      -5341.199      -6412.4073      1071.2083     -6552.7551      33.573175      1.9229648    
       120   262.66604     -5386.2386     -6442.9704      1056.7317     -6587.5483      29.85959       2.7124806    
       130   252.83384     -5422.5401     -6439.7159      1017.1758     -6580.4705      25.979344      1.2031596    
       140   253.85112     -5452.1837     -6473.4522      1021.2684     -6609.4826      26.071655      0.3058554    
       150   261.31822     -5490.4725     -6541.7819      1051.3093     -6646.6077      16.258824      6.9051021    
       160   255.73534     -5521.5936     -6550.4424      1028.8488     -6658.1373      19.717409      12.339682    
       170   253.42529     -5540.0941     -6559.6494      1019.5553     -6656.6678      23.293801      10.290221    
       180   248.51158     -5550.3253     -6550.1122      999.78691     -6661.4233      26.200127      3.4336075    
       190   250.80868     -5555.2555     -6564.2839      1009.0284     -6666.1644      25.536352      3.3494322    
SHAKE stats (type/ave/delta/count) on step 200
Bond:    4   1.111     1.81263e-06        9
Bond:    6   0.997     7.7941e-07         6
Bond:    8   1.08      1.08902e-06        7
Bond:   10   1.111     2.96498e-07        8
Bond:   12   1.08      4.69031e-07        9
Bond:   14   0.960001  0                  1
Bond:   18   0.957201  3.76468e-06     1280
Angle:  31   104.52    0.000411053      640
       200   251.50491     -5557.4253     -6569.2547      1011.8294     -6674.0854      24.804919      7.1387625    
Saving collective variables state to "out.colvars.state".
Loop time of 0.837922 on 1 procs for 100 steps with 2004 atoms

Performance: 20.622 ns/day, 1.164 hours/ns, 119.343 timesteps/s, 239.163 katom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.70731    | 0.70731    | 0.70731    |   0.0 | 84.41
Bond    | 0.0013939  | 0.0013939  | 0.0013939  |   0.0 |  0.17
Kspace  | 0.041896   | 0.041896   | 0.041896   |   0.0 |  5.00
Neigh   | 0.073708   | 0.073708   | 0.073708   |   0.0 |  8.80
Comm    | 0.002979   | 0.002979   | 0.002979   |   0.0 |  0.36
Output  | 0.00016374 | 0.00016374 | 0.00016374 |   0.0 |  0.02
Modify  | 0.009977   | 0.009977   | 0.009977   |   0.0 |  1.19
Other   |            | 0.0004913  |            |       |  0.06

Nlocal:           2004 ave        2004 max        2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          11159 ave       11159 max       11159 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         708083 ave      708083 max      708083 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708083
Ave neighs/atom = 353.33483
Ave special neighs/atom = 2.3403194
Neighbor list builds = 7
Dangerous builds = 0

fix 2 all colvars peptide.colvars input out.colvars.state output out2
----------------------------------------------------------------------
Initializing the collective variables module, version 2025-04-30.
Please cite Fiorin et al, Mol Phys 2013:
  https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Summary of compile-time features available in this build:
  - C++ language version: 201703
  - Multiple replicas: not available
  - Lepton custom functions: available
  - Tcl interpreter: not available
Using LAMMPS interface, version "2025-03-31".
Setting initial step number from MD engine: 200

run     100
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars":
# units = "" [default]
# smp = "cvcs" [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
  Initializing a new collective variable.
  # name = "one"
    Initializing a new "distance" component.
    # name = "" [default]
    # componentCoeff = 1 [default]
    # componentExp = 1 [default]
    # period = 0 [default]
    # wrapAround = 0 [default]
    # forceNoPBC = off [default]
    # scalable = on [default]
      Initializing atom group "group1".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group1" defined with 4 atoms requested.
      Initializing atom group "group2".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group2" defined with 1 atoms requested.
    # oneSiteSystemForce = off [default]
    # oneSiteTotalForce = off [default]
  All components initialized.
  # timeStepFactor = 1 [default]
  # width = 1 [default]
  # lowerBoundary = 0 [default]
  # upperBoundary = 1 [default]
  # hardLowerBoundary = on [default]
  # hardUpperBoundary = off [default]
  # expandBoundaries = off [default]
  # extendedLagrangian = off [default]
  # outputValue = on [default]
  # outputVelocity = off [default]
  # outputTotalForce = off [default]
  # outputAppliedForce = off [default]
  # subtractAppliedForce = off [default]
  # runAve = off [default]
  # corrFunc = off [default]
----------------------------------------------------------------------
  Initializing a new collective variable.
  # name = "two"
    Initializing a new "distance" component.
    # name = "" [default]
    # componentCoeff = 1 [default]
    # componentExp = 1 [default]
    # period = 0 [default]
    # wrapAround = 0 [default]
    # forceNoPBC = off [default]
    # scalable = on [default]
      Initializing atom group "group1".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group1" defined with 4 atoms requested.
      Initializing atom group "group2".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group2" defined with 1 atoms requested.
    # oneSiteSystemForce = off [default]
    # oneSiteTotalForce = off [default]
  All components initialized.
  # timeStepFactor = 1 [default]
  # width = 1 [default]
  # lowerBoundary = 0 [default]
  # upperBoundary = 1 [default]
  # hardLowerBoundary = on [default]
  # hardUpperBoundary = off [default]
  # expandBoundaries = off [default]
  # extendedLagrangian = off [default]
  # outputValue = on [default]
  # outputVelocity = off [default]
  # outputTotalForce = off [default]
  # outputAppliedForce = off [default]
  # subtractAppliedForce = off [default]
  # runAve = off [default]
  # corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 2 in total.
----------------------------------------------------------------------
  Initializing a new "harmonic" instance.
  # name = "h_pot"
  # colvars = { one, two }
  # stepZeroData = off [default]
  # outputEnergy = off [default]
  # outputFreq = 1000 [default]
  # timeStepFactor = 1 [default]
  # writeTISamples = off [default]
  # writeTIPMF = off [default]
  # centers = { 10, 10 }
  # targetCenters = { 10, 10 } [default]
  # outputCenters = off [default]
  # forceConstant = 100
  # decoupling = off [default]
  # targetForceConstant = -1 [default]
  The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
  The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 200, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
----------------------------------------------------------------------
Loading state from text file "out.colvars.state".
  Restarting collective variable "one" from value: 10.0128
  Restarting collective variable "two" from value: 9.62236
  Restarted harmonic bias "h_pot" with step number 200.
----------------------------------------------------------------------
The final output state file will be "out2.colvars.state".
SHAKE stats (type/ave/delta/count) on step 200
Bond:    4   1.111     1.81263e-06        9
Bond:    6   0.997     7.7941e-07         6
Bond:    8   1.08      1.08902e-06        7
Bond:   10   1.111     2.96498e-07        8
Bond:   12   1.08      4.69031e-07        9
Bond:   14   0.960001  0                  1
Bond:   18   0.957201  3.76468e-06     1280
Angle:  31   104.52    0.000411053      640
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
   Step          Temp          TotEng         PotEng         KinEng         E_pair         E_bond          f_2      
       200   251.50491     -5557.4253     -6569.2547      1011.8294     -6674.0854      24.804919      7.1387625    
       210   253.15308     -5538.5652     -6557.0253      1018.4601     -6672.0536      37.676597      0.61220051   
       220   245.19642     -5522.5163     -6508.966       986.44973     -6628.188       36.657689      0.048643226  
       230   258.69807     -5495.731      -6536.4992      1040.7682     -6658.289       34.857874      0.22091688   
       240   260.79678     -5469.8717     -6519.0832      1049.2115     -6624.1856      31.576948      3.7574906    
       250   269.07478     -5438.3946     -6520.9093      1082.5147     -6616.4361      25.44764       8.6600558    
       260   266.011       -5397.3478     -6467.5366      1070.1888     -6580.2908      26.871876      8.3323545    
       270   272.81289     -5350.8824     -6448.4359      1097.5535     -6563.8224      23.114152      10.973141    
       280   279.42318     -5307.9786     -6432.126       1124.1474     -6557.3377      33.643935      8.5490101    
       290   286.8495      -5260.8412     -6414.8654      1154.0242     -6515.6708      28.574747      5.9100395    
SHAKE stats (type/ave/delta/count) on step 300
Bond:    4   1.111     1.79797e-05        9
Bond:    6   0.997005  1.02517e-05        6
Bond:    8   1.08      1.85102e-05        7
Bond:   10   1.111     9.98838e-06        8
Bond:   12   1.08      8.8411e-06         9
Bond:   14   0.960008  0                  1
Bond:   18   0.957203  1.84466e-05     1280
Angle:  31   104.52    0.00168371       640
       300   291.527       -5216.2851     -6389.1273      1172.8423     -6503.1206      27.889003      2.2482527    
Saving collective variables state to "out2.colvars.state".
Loop time of 0.852557 on 1 procs for 100 steps with 2004 atoms

Performance: 20.268 ns/day, 1.184 hours/ns, 117.294 timesteps/s, 235.058 katom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.71436    | 0.71436    | 0.71436    |   0.0 | 83.79
Bond    | 0.0013938  | 0.0013938  | 0.0013938  |   0.0 |  0.16
Kspace  | 0.042703   | 0.042703   | 0.042703   |   0.0 |  5.01
Neigh   | 0.080418   | 0.080418   | 0.080418   |   0.0 |  9.43
Comm    | 0.0030098  | 0.0030098  | 0.0030098  |   0.0 |  0.35
Output  | 0.00011964 | 0.00011964 | 0.00011964 |   0.0 |  0.01
Modify  | 0.010058   | 0.010058   | 0.010058   |   0.0 |  1.18
Other   |            | 0.0004936  |            |       |  0.06

Nlocal:           2004 ave        2004 max        2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          11296 ave       11296 max       11296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         708152 ave      708152 max      708152 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708152
Ave neighs/atom = 353.36926
Ave special neighs/atom = 2.3403194
Neighbor list builds = 8
Dangerous builds = 0

Total wall time: 0:00:02
